TY - JOUR
T1 - PRALINE: a versatile multiple sequence alignment toolkit.
AU - Bawono, P.
AU - Heringa, J.
PY - 2014
Y1 - 2014
N2 - Profile ALIgNmEnt (PRALINE) is a versatile multiple sequence alignment toolkit. In its main alignment protocol, PRALINE follows the global progressive alignment algorithm. It provides various alignment optimization strategies to address the different situations that call for protein multiple sequence alignment: global profile preprocessing, homology-extended alignment, secondary structure-guided alignment, and transmembrane aware alignment. A number of combinations of these strategies are enabled as well. PRALINE is accessible via the online server http://www.ibi.vu.nl/programs/PRALINEwww/. The server facilitates extensive visualization possibilities aiding the interpretation of alignments generated, which can be written out in pdf format for publication purposes. PRALINE also allows the sequences in the alignment to be represented in a dendrogram to show their mutual relationships according to the alignment. The chapter ends with a discussion of various issues occurring in multiple sequence alignment. © 2014 Springer Science+Business Media, LLC.
AB - Profile ALIgNmEnt (PRALINE) is a versatile multiple sequence alignment toolkit. In its main alignment protocol, PRALINE follows the global progressive alignment algorithm. It provides various alignment optimization strategies to address the different situations that call for protein multiple sequence alignment: global profile preprocessing, homology-extended alignment, secondary structure-guided alignment, and transmembrane aware alignment. A number of combinations of these strategies are enabled as well. PRALINE is accessible via the online server http://www.ibi.vu.nl/programs/PRALINEwww/. The server facilitates extensive visualization possibilities aiding the interpretation of alignments generated, which can be written out in pdf format for publication purposes. PRALINE also allows the sequences in the alignment to be represented in a dendrogram to show their mutual relationships according to the alignment. The chapter ends with a discussion of various issues occurring in multiple sequence alignment. © 2014 Springer Science+Business Media, LLC.
U2 - 10.1007/978-1-62703-646-7_16
DO - 10.1007/978-1-62703-646-7_16
M3 - Article
SN - 1064-3745
VL - 10709
SP - 245
EP - 262
JO - Methods in Molecular Biology
JF - Methods in Molecular Biology
ER -